Fig. 2

Graphic interface for VCFtoTree. From left to right, and from top to bottom are the interfaces of VCFtoTree. a Choose species that you want to study; b Provide the address (URL or local address) of your reference genome, vcf file, and enter the number of samples in your vcf file; c Enter your target region; d When you choose human in the main menu, you will be directed to this window to choose the dataset that you want to include in your alignment. “Human-1000Genomes” directly uses 1000 Genomes Phase 3 data, while you can use your own vcf file by choosing “Human-Custom”; e If you choose “Human-1000Genomes”, you will be directed to this window to choose the populations; f. Choose the phylogenetic tool you want to use for tree building. If neither were chosen, the program will only output the alignment